Sudeep Sarma

Unified Sampling and Ranking for Protein Docking with DFMDock

DFMDock is a diffusion model for protein docking that combines generative sampling and energy-based ranking, achieving higher success rates than existing methods.

Can We Extract Physics-like Energies from Generative Protein Diffusion Models?

This paper examines whether diffusion models can extract physics-like energies for protein docking, finding they can recover energy funnels comparable to Rosetta in 9 out of 25 cases.

Designed Peptides as Affinity Ligands for Extracellular-Vesicle-based Cancer Biomarker Detection

The paper designs peptides as alternatives to antibodies for detecting protein biomarkers on extracellular vesicles, showing comparable affinity to antibodies.

Development of MHC Class I Blocking Peptides to Target Metabolic Dysfunction-Associated Steatohepatitis CD8+ T Cell Activation

The paper develops MHC class I blocking peptides to inhibit CD8+ T cell activation in MASH, reducing inflammation and fibrosis.